Patterns Of Geographic Variation Research Articles

CattleAssigner: A framework for accurate assignment of individuals to cattle lineages and populations using minimum informative markers

Assigning individual animals to their respective breeds, populations or lineages has immense significance in the evolutionary analyses of global cattle populations besides detecting the underlying genetic variation that may likely have facilitated the adaptation of these breeds to diverse environmental conditions. It is also important in discovering the geographic patterns of genetic variation in cattle populations as well as tracing the geographical origin of breeds, food products, and diseases. Given this, the present study was undertaken to elucidate the minimum number of informative single nucleotide polymorphism (SNP) markers, originally generated using medium-density BovineSNP50 BeadChip across 1823 individuals represnting 73 populations, to assign individual animals to the corresponding lineage/group (African or European or Indicine or admixed) and respective populations within that lineage/group using two well-known supervised machine learning (ML) algorithms namely Random Forest (RF) and Extreme Gradient Boosting (XGBoost). Each of the two ML models were trained with the most informative SNP panels (with sizes of 48, 96, and 192) that were elucidated using two statistical methods i.e., principal component analysis (PCA) and Wright's fixation index (FST), and two ML methods (RF with Gini, and RF with MDA). Three panels with the topmost discriminant SNPs (at 192, 96, and 48 densities) were created for each of the marker preselection approaches. These panels were evaluated, based on their performance vis-à-vis animals’ assignment to respective lineage, population group or population. The results showed that XGBoost achieved the best accuracy of 95% with 192-SNP panel (selected via RF with MDA), followed by RF (93% accuracy) with 192-SNP panel (selected via RF with either Gini or MDA), for animal to lineage assignment. Similarly, RF trained with 48-SNP panel (selected via RF with Gini algorithm) achieved the best accuracy of 97% for assigning animals to African lineage, while it achieved the best accuracy of 89% for assigning animals to admixed populations using 96-SNP panel (selected via PCA). On the other hand, XGBoost achieved the best accuracy of 88% for assigning animals to European breeds using 192-SNP panel (selected via FST method). Furthermore, the results with both RF and XGBoost achieved a poor performance of assigning animals of Indicine lineage to the correct group as the best accuracy for such assignment was 66%, achieved using RF with 192-SNP panel (selected via FST method). In conclusion, the study reports the applicability of statistical and ML approaches for identification of discriminatory SNPs, useful the assignment of individuals to corresponding lineages and to respective populations within lineages besides revealing the efficiency of XGBoost and RF-based ML models in performing such assignments. Both the ML models achieved better performance as compared to statistical ones in assigning the animals to specific lineages while they faired comparably similar to each other for the assignment of individuals to respective populations within respective lineages or population groups.

Geography and associated bioclimatic factors differentially affect leaf phenolics in three ivy species (Hedera L.) across the Iberian Peninsula

The biosynthesis of secondary metabolites in plants, especially that of phenolic compounds, is stimulated to protect against several environmental stress factors such as cold temperatures, drought, and UV-irradiance. As a result, when a species occurs under different climatic conditions, differences in phenolic accumulation are expected across species distribution in response to the environmental cues. However, our understanding of phenolic compounds' natural variation is limited, as most of our knowledge on secondary metabolite biosynthesis stems from experimental studies conducted under controlled conditions. In this study we analyze phenolic content and its relation to climatic and geographic variation in three closely related Hedera species (H. helix, H. hibernica and H. iberica) across their southwestern range limits in the Iberian Peninsula (82 populations, 401 individuals). The Iberian Peninsula concentrates the highest global species richness of Hedera, with the three species sharing range boundaries along the latitudinal and longitudinal climatic gradient of the region. We found that the three species exhibited different climatic and geographic patterns of phenolic content variation in the study area. The phenolic production in H. helix increased with elevation in relation to the decrease of temperature and the increase of temperature contrast, whereas in H. hibernica varies with latitude in relation to summer temperature and precipitation regimes, increasing in areas with no summer drought. In contrast, we did not find any environmental variables associated with phenolic content in H. iberica, likely due to its narrow geographic and climatic range and a higher influence of microclimatic conditions. Although the three Hedera species are closely related, our results suggest that leaf phenolic production may be triggered by different environmental conditions in each species. Our study underscores the species-specific nature of phenolic compounds' role in plant stress response.

Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

Sexual color ornamentation, microhabitat choice, and thermal physiology in the common wall lizard (Podarcis muralis).

Common wall lizards (Podarcis muralis) in Italy show a striking variation in body coloration across the landscape, with highly exaggerated black and green colors in hot and dry climates and brown and white colors in cool and wet climates. Males are more intensely colored than females, and previous work has suggested that the maintenance of variation in coloration across the landscape reflects climatic effects on the strength of male-male competition, and through this sexual selection. However climatic effects on the intensity of male-male competition would need to be exceptionally strong to fully explain the geographic patterns of color variation. Thus, additional processes may contribute to the maintenance of color variation. Here we test the hypothesis that selection for green and black ornamentation in the context of male-male competition is opposed by selection against ornamentation because the genes involved in the regulation of coloration have pleiotropic effects on thermal physiology, such that ornamentation is selected against in cool climates. Field observations revealed no association between body coloration and microhabitat use or field active body temperatures. Consistent with these field data, lizards at the extreme ends of the phenotypic distribution for body coloration did not show any differences in critical minimum temperature, preferred body temperature, temperature-dependent metabolic rate, or evaporative water loss when tested in the laboratory. Combined, these results provide no evidence that genes that underlie sexual ornamentation are selected against in cool climate because of pleiotropic effects on thermal biology.

Testing for variation in photoperiodic plasticity in a butterfly: Inconsistent effects of circadian genes between geographic scales.

The genetic components of the circadian clock have been implicated as involved in photoperiodic regulation of winter diapause across various insect groups, thereby contributing to adaptation to adverse seasonal conditions. So far, the effects of within-population variation in these genes have not been well explored. Here, we present an experimental test of the effects of within-population variation at two circadian genes, timeless and period, on photoperiodic responses in the butterfly Pararge aegeria. While nonsynonymous candidate SNPs in both of these genes have previously shown to be associated with diapause induction on a between-population level, in the present experiment no such effect was found on a within-population level. In trying to reconcile these results, we examine sequence data, revealing considerable, previously unknown protein-level variation at both timeless and period across Scandinavian populations, including variants unique to the population studied here. Hence, we hypothesize that these variants may counteract the previously observed diapause-averting effect of the candidate SNPs, possibly explaining the difference in results between the experiments. Whatever the cause, these results highlight how the effects of candidate SNPs may sometimes vary across genetic backgrounds, which complicates evolutionary interpretations of geographic patterns of genetic variation.

Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex.

Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex. We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex. We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades. Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.

Genetic Diversity and Population Structure of Chinese Longsnout Catfish (Leiocassis longirostris) Using Microsatellite DNA Markers

The Chinese longsnout catfish (Leiocassis longirostris) is an economically important freshwater fish in China; however, its wild resources have declined dramatically in recent decades. Understanding the genetic structure of Chinese longsnout catfish populations is crucial to guide breeding programs and fishy restoration. In this study, 15 highly polymorphic microsatellite DNA loci were used to evaluate its genetic diversity and population structure. Chinese longsnout catfish populations show high genetic diversity; they do not show significant genetic differentiation or systematic geographic pattern of variation. From the upper to the lower reaches of the Yangtze River, the genetic diversity of Chinese longsnout catfish populations showed an increasing trend. The Gezhouba and Three Gorges dams, which physically divide the Yangtze River into upstream and mid-downstream sections, did not contribute to the genetic differentiation of Chinese longsnout catfish populations. Hence, the source of broodstock is not critical for within-river breeding programs and stock enhancement to restore the wild population. In addition, possible effects of dams on differentiation among populations are crucial and long-term evaluation is essential.

Genomic insights into differentiation and adaptation of Amorphophallus yunnanensis in the mountainous region of Southwest China.

The role of geographical isolation and environmental adaptation in driving the differentiation and radiation of species has been a hotspot in evolutionary biology. The extremely complicated and fragmented geography of the mountainous region of Southwest China provides an excellent system for investigating the process of species divergence in heterogeneous habitats. Amorphophallus yunnanensis is a species of extreme habitat preference that resides mainly in the mountainous region of Southwest China. Here, we used restriction site-associated DNA sequencing (RAD-seq) to characterize the geographic pattern of genetic variation among 19 populations of A. yunnanensis as well as the genomic basis of environmental adaptation. A pattern of low population genetic diversity and high level of genetic differentiation was observed. The genomic data revealed a clear east-west genetic differentiation, with two distinct genetic lineages corresponding to the Guizhou plateau and Yunnan plateau, respectively. However, we discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Significant levels of isolation by distance along with isolation by environment were detected. Outlier tests and genome-environment association analyses identified 89 putatively adaptive loci that might play a role in environmental adaptation. Our results suggest that the genetic divergence of A. yunnanensis is attributed to geographical isolation together with divergent selection in the mountainous region of Southwest China.

Can Bergmann’s Rule and the Thermal Melanism Hypothesis explain the variation in colour and size observed in the wild bee Eoanthidium insulare (Apoidea: Megachilidae) across its Palaearctic range?

To analyse geographic variation patterns and assess the applicability of biogeographical rules in insects, the West Palaearctic anthidiine bee Eoanthidium insulare serves as an excellent model. This species showcases a highly variable black-and-yellow colour pattern, with a distribution spanning over 4400 km from the Adriatic Sea to the Pamir Mountains and extending over 1660 km in a south-north direction. We examined 214 specimens from all geographic regions of its distribution and identified a significant increase in both body size and the proportion of black in the integument from south to north. This phenomenon may be attributed to a more efficient exploitation of solar energy through a larger integument surface area (Bergmann’s Rule) and enhanced heat retention due to lower skin reflectance (Thermal Melanism Hypothesis). These two processes, therefore, complement each other. However, despite the cooler climates at higher altitudes, we found no correlations between body size and altitude. Furthermore, while we observed an increase in the proportion of black in the integument from east to west, there was no significant increase in body size. Notably, no correlation between body size and body colouration was identified, suggesting that size and colour adaptation are independent processes. Given that the various colour and size patterns were identified as clinal rather than discontinuous, and the intraspecific genetic distance across the distribution area was remarkably low (0.00138), featuring only four distinct haplotypes of the mitochondrial COI region DNA sequence, we suggest that the subspecies E. i. persicolum and E. i. lemesium be regarded as synonymous with the nominate subspecies (syn. nov.). These findings suggest that, although Bergmann’s Rule and the Thermal Melanism Hypothesis can account for certain aspects of geographic variation in the body size and colouration of E. insulare, their effects may be influenced or superimposed by factors such as genetic constitution.

Layers of Folkloric Variation: Computational Explorations of Poetic and Narrative Text Corpora

Variation is a core feature of folklore that plays a part in configuring the processes of folkloric communication, transmission and creativity. Computational analysis of large folklore collections offers new outlooks on the study of variation. The article explores the nature of folkloric variation on the basis of folk song and fairy tale text corpora from the Estonian Folklore Archives. Our enquiry into regional variation in Estonian folk song showed different patterns of geographic variation for metre, repertoire and language. To investigate further the possibilities to disassemble the components of variation we turned to a smaller corpus of fairy tale texts from the distinct Seto language community. The results of stylometric analysis of fairy tales collected within the close language community as a rule found that word usage patterns in stories told by the same storytellers were closer to each other than stories with the same content (i.e. tale types). However, other factors, such as collectors’ individual styles, recording time, length of text, and storyteller’s place of origin contributed notably to similarity as per stylometric scores. The study has shown that the individual features and aspects of such a complex phenomenon as folklore can follow its own variation patterns. Computational analysis of the variation in large text corpora helps us get a better understanding of the functioning of variation, and the processes of folkloric creation. However, the layers of folkloric variation are not that easy to disassemble, one must be aware of the biases in text corpora and keep in mind the effect of the linguistic variation on the results.

Integrative revision of species limits in the genus Schiffornis (Aves: Tityridae) reveals cryptic diversity in the Neotropics

Abstract Accurate species delimitation is essential for many biological subdisciplines. Nonetheless, current species diversity remains incompletely documented even in well-studied groups such as birds. Here, we take an integrative approach to examine species limits in the genus Schiffornis, a widespread group of dull-plumaged, whistle-voiced suboscine passerines of Neotropical humid-forest understory, currently considered to comprise seven species. We measured geographic variation in song, morphology, and mitochondrial and genome-wide nuclear markers to resolve the taxonomy of the genus. We show that Schiffornis comprises 13 separately evolving population lineages, of which most qualify as species taxa under all species definitions. These include a cryptic new species, several species splits, and the resurrection of a morphologically undifferentiated, but vocally and genetically distinct, taxon that was synonymized nearly a century ago in the Schiffornis turdina complex. We also found several hitherto unnoticed contact zones between diverging lineages and a leapfrog pattern of geographic song variation in the S. turdina complex, and we highlight potential avenues of further research of this genus.

Geographical provenance variation of growth and wood properties of 18-year-old Schima superba.

We analyzed the variation patterns of growth and wood properties of 24 different provenances of 18-year-old Schima superba in Jian'ou, Fujian Province. A total of 11 growth and wood indices were measured, including tree height, diameter at breast height, wood basic density and anatomical structure. We analyzed the geographical variation patterns of growth and wood properties, and the provenance areas were divided. Further, the excellent timber provenances were selected according to different uses. The results showed that the variation of growth traits, which was 17.6%-27.3% with mean value of 22.4%, was larger than that of wood properties (7.0%-21.0%, mean 12.7%). Growth properties and some wood properties (fiber length, fiber lumen diameter and fiber cell wall thickness) had significant differences among provenances. Growth traits were not correlated with fiber traits, and they could be selected independently without emphasis on other traits. There was significant correlation between the longitudinal and radial growth indicators of wood properties, but they were not correlated with the wood basic density, which could be selected independently. In addition, the growth and wood properties were significantly influenced by temperature and precipitation, which showed a latitudinal variation pattern. According to Q-type clustering analysis, 24 provenances could be divided into four categories, of which southern provenances from distribution area of S. superba had vigorous growth and supper wood properties. They had smaller microfibril angle, higher maturity, longer fiber length, and thicker fiber cell wall. Finally, five excellent provenances were selected according to pulpwood and building use.

Temperature is a cryptic factor shaping the geographical pattern of genetic variation in Ceratophyllum demersum across a subtropical freshwater lake

Macrophyte habitats exhibit remarkable heterogeneity, encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors. Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants. However, the links among genetic diversity, epigenetic variation, and environmental variables remain largely unclear, especially for clonal aquatic plants. Here, we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort (Ceratophyllum demersum) in a subtropical lake. Environmental factors were highly correlated with the genetic and epigenetic variation of C. demersum, with temperature being a key driver of the genetic variation. Lower temperature was detected to be correlated with greater genetic and epigenetic variation. Genetic and epigenetic variation were positively driven by water temperature, but were negatively affected by ambient air temperature. These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions, and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.

Range-wide phylogenomics of the Great Horned Owl (Bubo virginianus) reveals deep north-south divergence in northern Peru.

The Great Horned Owl (Bubo virginianus) inhabits myriad habitats throughout the Americas and shows complex patterns of individual and geographic morphological variation. The owl family Strigidae is known to follow ecogeographic rules, such as Gloger's rule. Although untested at the species level, these ecogeographic rules may affect B. virginianus plumage coloration and body size. Previous studies have indicated that, despite this species' morphological variability, little genetic differentiation exists across parts of their range. This study uses reduced representation genome-wide nuclear and complete mitochondrial DNA sequence data to assess range-wide relationships among B. virginianus populations and the disputed species status of B. v. magellanicus (Magellanic or Lesser Horned Owl) of the central and southern Andes. We found shallow phylogenetic relationships generally structured latitudinally to the north of the central Andes, and a deep divergence between a southern and northern clade close to the Marañón Valley in the central Andes, a common biogeographic barrier. We identify evidence of gene flow between B. v. magellanicus and other subspecies based on mitonuclear discordance and F-branch statistics. Overall differences in morphology, plumage coloration, voice, and genomic divergence support species status for B. v. magellanicus.

Molecular species delimitation reveals hidden endemism in Faxonius placidus (Hagen 1870) (Decapoda: Astacidea: Cambaridae) in southeastern USA

Abstract Molecular surveys are critical for understanding species boundaries and evolutionary relationships of North American crayfishes, as traditional morphological characters used for taxonomy frequently misrepresent crayfish diversity. The bigclaw crayfish, Faxonius placidus (Hagen, 1870), is currently described as a widely distributed crayfish that is common throughout the Cumberland, Tennessee, and Lower Ohio river drainages. The geographic distribution of F. placidus is based on identifications using traditional morphological characters including the first-form male gonopod, chelae, and rostrum. Within F. placidus, color pattern variation is specific to populations separated by hydrogeographic barriers. We used DNA barcoding data (mtDNA-COI) and genome-wide molecular markers (nuclear SNPs) to examine geographic patterns of genetic variation in F. placidus within the Cumberland and Tennessee river drainages. The federally endangered Nashville crayfish, F. shoupi (Hobbs, 1948), was included in our analyses, as previous phylogenetic reconstructions suggest F. placidus is paraphyletic with respect to F. shoupi. Phylogenetic reconstructions and molecular species delimitation identified four genetically distinct lineages within F. placidus that are paraphyletic with respect to F. shoupi. Our results add to numerous studies demonstrating the utility of robust molecular analyses for understanding the biodiversity of North American crayfishes.

#4424 FREQUENCY OF RED BLOOD CELL TRANSFUSION USE IN PATIENTS WITH ANEMIA OF CHRONIC KIDNEY DISEASE (CKD) IN EUROPE: A SYSTEMATIC LITERATURE REVIEW

Abstract Background and Aims Anemia of CKD is common and managed with oral or intravenous iron, erythropoiesis-stimulating agents (ESAs) and, when necessary, red blood cell transfusions (RBCT). Reducing RBCT use is a goal in the management of anemia of CKD due to known short term (e.g., hyperkalaemia, heart failure) and longer term risks (e.g., allosensitization), but there is limited collated data on their use in Europe. A systematic literature review was conducted to evaluate the frequency of RBCT use among dialysis dependent (DD) and non-dialysis (ND) patients, and associated data reported for predictors of RBCT receipt, complications, healthcare resource use (HCRU), and costs. Method A comprehensive search strategy was used to retrieve real-world (RW) studies and randomized controlled trials (RCTs) conducted in DD and ND CKD patients with anemia using Embase and Medline (1980 to June 2022). Searches of conference abstracts, bibliographies and grey literature were also conducted. Studies which included European patients’ data are described here. Results Of the 3495 citations retrieved, 182 relevant studies were identified including 54 studies with European patients. Thirteen were RW studies including 12 quantifying the frequency of RBCT use (Table). In RW studies, the overall frequency of RBCT use ranged from 4.3–35.0% across studies and for key subgroups (n=10 studies: DD only studies, 8.4–33.9%; ND only studies, 4.3–35.0%). The number of RBCT units per patient-year (PY) ranged from 1.4–2.7 among DD patients (n=2 studies; no ND studies found). RBCT use appeared to vary by patient factors (iron/ESA use, CKD stage), by study design (e.g., length of follow-up) and across countries (but with no clear patterns in geographic variation). For the 41 RCTs including European patients (single country, n=3 studies, multi-country, n=38 studies), the overall frequency of RBCT use ranged from 0–21.6% (DD only studies, 0.4–21.6%; ND only studies, 0–14.8%), which was lower than those recorded in the RW studies. The rate of RBCT use in trials ranged from 3.5–66.0 events per 100 PY overall (DD only studies, 3.5–66.0; ND only study, 8.0); the number of RBCT units per PY ranged from 0.20–1.65 among DD patients (n=2 studies; no ND studies found). No studies used statistical modelling to quantify predictors of RBCT use while adjusting for potential differences between groups. One RW study from 1986 reported detection of human T-lymphotropic virus type III (HTLV-III; subsequently known as HIV) antibodies in 4 patients who had received RBCT (in a sample of 276 screened chronic HD patients). Of three RW studies reporting data on costs, two were >30 years old and one provided costs relating to receipt of inpatient RBCT in ND patients stratified by oral iron, low dose, or high dose intravenous iron use from 2013–2015 (n=111). Conclusion RBCT use forms part of the management of anemia of CKD in Europe and its use is variable but not infrequent. RBCT risk in RW studies appeared elevated compared to RCTs. There were no consistent patterns in geographic variation, but risk varied by patient factors and study design. There is currently limited European data reporting on frequency of associated complications, predictors of RBCT use, associated HCRU and costs. Funding: GSK (Study 218929).

Convergent genomic signatures of local adaptation across a continental-scale environmental gradient.

Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.

Global patterns of taxonomic and phylogenetic diversity of flowering plants: Biodiversity hotspots and coldspots

Species diversity of angiosperms (flowering plants) varies greatly among regions. Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes. Here, using a comprehensive data set for regional angiosperm floras across the world, we show geographic patterns of taxonomic (species) diversity, phylogenetic diversity, phylogenetic dispersion, and phylogenetic deviation (i.e., phylogenetic diversity after accounting for taxonomic diversity) across the world. Phylogenetic diversity is strongly and positively correlated with taxonomic diversity; as a result, geographic patterns of taxonomic and phylogenetic diversity across the world are highly similar. Areas with high taxonomic and phylogenetic diversity are located in tropical regions whereas areas with low taxonomic and phylogenetic diversity are located in temperate regions, particularly in Eurasia and North America, and in northern Africa. Similarly, phylogenetic dispersion is, in general, higher in tropical regions and lower in temperate regions. However, the geographic pattern of phylogenetic deviation differs substantially from those of taxonomic and phylogenetic diversity and phylogenetic dispersion. As a result, hotspots and coldspots of angiosperm diversity identified based on taxonomic and phylogenetic diversity and phylogenetic dispersion are incongruent with those identified based on phylogenetic deviations. Each of these metrics may be considered when selecting areas to be protected for their biodiversity.

Population bottleneck associated with but likely preceded the recent evolution of self-fertilization in a coastal dune plant.

Evolution of self-fertilization may be initiated by a historical population bottleneck, which should diagnostically reduce lineage-wide genetic variation. However, selfing can also strongly reduce genetic variation after it evolves. Distinguishing process from pattern is less problematic if mating system divergence is recent and geographically simple. Dramatically reduced diversity is associated with the transition from outcrossing to selfing in the Pacific coastal endemic Abronia umbellata that includes large-flowered, self-incompatible populations (var. umbellata) south of San Francisco Bay and small-flowered, autogamous populations (var. breviflora) to the north. Compared to umbellata, synonymous nucleotide diversity across 10 single-copy nuclear genes was reduced by 94% within individual populations and 90% across the whole selfing breviflora lineage, which contained no unique polymorphisms. The geographic pattern of genetic variation is consistent with a single origin of selfing that occurred recently (7-28 kya). These results are best explained by a historical bottleneck, but the two most northerly umbellata populations also contained little variation and clustered with selfing populations, suggesting that substantial diversity loss preceded the origin of selfing. A bottleneck may have set the stage for the eventual evolution of selfing by purging genetic load that prevents the spread of selfing.

Flower morphology variation in five species of Penstemon (Plantaginaceae) displaying Hymenoptera pollination syndrome

Background: Geographic distance promotes phenotypic variation by facilitating environmental distance, limiting gene flow, and exposing plants to different pollen vectors. Therefore, understanding how plant morphology changes across a geographic range improves our understanding of the drivers of morphological diversification both on a macro- and micro-evolutionary scale.
 Questions: 1) How do geographic location and abiotic factors affect flower morphology between populations? 2) Is there a geographic pattern of flower morphology variation? and 3) How does yearly variation in temperature and precipitation affect flower morphology within populations?
 Studied species: Penstemon albidus, P. fruticosus, P. glandulosus, P. speciosus, and P. whippleanus
 Study site and dates: The continental USA, summers of 2017 and 2018
 Methods: Fifty-seven populations and 496 individuals were selected at random to measure ten floral traits. Bioclimatic variables were extracted from the WorldClim database and NOAA. Linear models, partial least squares regression, Mantel tests and canonical correlation analysis were used to analyze the data.
 Results: Geographic variables alone explained a significant portion of the variation in flower morphology in two species, while in others, flower morphology did not vary despite large geographic distances. Penstemon albidus and P. whippleanus flowers increase in size from south-north, while P. glandulosus and P. speciosus exhibited an east-west increasing trend. Additionally, mean annual precipitation was the most important variable influencing P. glandulosusflower morphology.
 Conclusions: Geographic distance facilitates isolation-by-distance and isolation-by-phenology as well as abiotic differences between populations; however, other factors such as pollinators might be keeping populations morphologically homogeneous despite large geographic distance.